tRNADB-CE: tRNA gene database curated manually by experts.
tRNADB-CE: tRNA gene database curated manually by experts.
复制标题
DOI：
10.1093/nar/gkn692
复制
发表时间：
2009-01
影响因子：
14.9
通讯作者：
Inokuchi H
中科院分区：
文献类型：
--
作者：
Abe T;Ikemura T;Ohara Y;Uehara H;Kinouchi M;Kanaya S;Yamada Y;Muto A;Inokuchi H
我们通过分析DDBJ/EMBL/GenBank中的534个原核生物完整基因组和394个WGS（Whole Genome Shotgun）分割的基因组草图以及从宏基因组分析中获得的约620万个DNA片段序列，构建了一个新的大规模tRNA基因数据库。通过运行三个计算机程序来进行对tRNA基因的详尽搜索，以提高预测的完整性和准确性。从分析的这些原核生物基因组中获得的候选tRNA基因总数的1.4%发现三个程序之间的分配不一致。不一致的病例由tRNA实验领域的专家手动检查。结果表明，在tRNADB-CE数据库中共登记了144061个tRNA基因，是tRNAscan-SE全基因组分析数据库中已报道基因数的4倍多。tRNADB-CE允许浏览序列信息、三叶草结构和所有tRNA基因之间的相似性搜索结果。对于每个完整的基因组，可以浏览各个反密码子的tRNA基因的数量和所有蛋白质基因中的密码子使用频率以及各个tRNA基因在每个基因组中的定位。tRNADB-CE可在http://trna.nagahama-i-bio.ac.jp上免费访问。
We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and approximately 6.2 million DNA fragment sequences obtained from metagenomic analyses. This exhaustive search for tRNA genes was performed by running three computer programs to enhance completeness and accuracy of the prediction. Discordances of assignment among three programs were found for ∼4% of the total of tRNA gene candidates obtained from these prokaryote genomes analyzed. The discordant cases were manually checked by experts in the tRNA experimental field. In total, 144 061 tRNA genes were registered in the database ‘tRNADB-CE’, and the number of the genes was more than four times of that of the genes previously reported by the database from analyses of complete genomes with tRNAscan-SE program. The tRNADB-CE allows for browsing sequence information, cloverleaf structures and results of similarity searches among all tRNA genes. For each of the complete genomes, the number of tRNA genes for individual anticodons and the codon usage frequency in all protein genes and the positioning of individual tRNA genes in each genome can be browsed. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp.
登录
查看更多内容
影响因子：
56.9
作者：
Venter, JC;Remington, K;Smith, HO
通讯作者：
Smith, HO
影响因子：
14.9
作者：
Dunin-Horkawicz, Stanislaw;Czerwoniec, Anna;Gajda, Michal J.;Feder, Marcin;Grosjean, Henri;Bujnicki, Janusz M.
通讯作者：
Bujnicki, Janusz M.
影响因子：
14.9
作者：
Maglott, Donna;Ostell, Jim;Pruitt, Kim D;Tatusova, Tatiana
通讯作者：
Tatusova, Tatiana
影响因子：
14.9
作者：
Griffiths-Jones S;Moxon S;Marshall M;Khanna A;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
THOMPSON, JD;HIGGINS, DG;GIBSON, TJ
通讯作者：
GIBSON, TJ